%WAVELET  1D Wavelet transform with optional significance testing
%
%   [WAVE,PERIOD,SCALE,COI,DJ,PARAMOUT,K] = contwt(Y,DT,PAD,DJ,S0,J1,MOTHER,PARAM)
%
%   Computes the continuous wavelet transform of the vector Y (length N),
%   with sampling rate DT.
%
%   By default, the Morlet wavelet (k0=6) is used.
%   The wavelet basis is normalized to have total energy=1 at all scales.
%
%  
% OBLIGATORY INPUTS:
%
%    Y = the time series of length N.
%    DT = amount of time between each Y value, i.e. the sampling time.
%
% OUTPUTS:
%
%    WAVE is the WAVELET transform of Y. This is a complex array
%    of dimensions (N,J1+1). FLOAT(WAVE) gives the WAVELET amplitude,
%    ATAN(IMAGINARY(WAVE),FLOAT(WAVE) gives the WAVELET phase.
%    The WAVELET power spectrum is ABS(WAVE)^2.
%    Its units are sigma^2 (the time series variance).
%
%
% OPTIONAL INPUTS:
% 
% *** Note *** setting any of the following to -1 will cause the default
%               value to be used.
%
%    PAD = if set to 1 (default is 0), pad time series with enough zeroes to get
%         N up to the next higher power of 2. This prevents wraparound
%         from the end of the time series to the beginning, and also
%         speeds up the FFT's used to do the wavelet transform.
%         This will not eliminate all edge effects (see COI below).
%           Enter [] for default.
%
%    DJ = the spacing between discrete scales. Default is 0.25.
%         A smaller # will give better scale resolution, but be slower to plot.
%          Enter [] for default.
%
%    S0 = the smallest scale of the wavelet.   Default is 2*DT. Enter [] for default.
%
%    J1 = the # of scales minus one. Scales range from S0 up to S0*2^(J1*DJ),
%        to give a total of (J1+1) scales. Default is J1 = (LOG2(N DT/S0))/DJ.
%         Enter [] for default.
%
%    MOTHER = the mother wavelet function.
%             The choices are 'MORLET', 'PAUL', or 'DOG'
%
%    PARAM = the mother wavelet parameter.
%            For 'MORLET' they are:
%               - k0 (wavenumber), default is 6;
%               - sigmat (parameter of the Gaussian window), default is 1.
%            For 'PAUL' this is m (order), default is 4.
%            For 'DOG' this is m (m-th derivative), default is 2.
%
%
% OPTIONAL OUTPUTS:
%
%    PERIOD = the vector of "Fourier" periods (in time units) that corresponds
%           to the SCALEs.
%
%    SCALE = the vector of scale indices, given by S0*2^(j*DJ), j=0...J1
%            where J1+1 is the total # of scales.
%
%    COI = if specified, then return the Cone-of-Influence, which is a vector
%        of N points that contains the maximum period of useful information
%        at that particular time.
%        Periods greater than this are subject to edge effects.
%        This can be used to plot COI lines on a contour plot by doing:
%
%              contour(time,log(period),log(power))
%              plot(time,log(coi),'k')
%    DJ = actual scale spacing used
%
%    PARAMOUT = actual parameter value used for mother wavelet
%    
%   K       =  frequencies at which the transform was computed
% 
% ------------------------
% Last modified: Jon Erickson, Oct 14, 2014. 
%    -changed default J1 to be the ceiling instead of fix(...)
%    -changed default input args handling
% 
% Original code by:
%----------------------------------------------------------------------------
%   Copyright (C) 1995-2004, Christopher Torrence and Gilbert P. Compo
%
%   This software may be used, copied, or redistributed as long as it is not
%   sold and this copyright notice is reproduced on each copy made. This
%   routine is provided as is without any express or implied warranties
%   whatsoever.
%
% Notice: Please acknowledge the use of the above software in any publications:
%    ``Wavelet software was provided by C. Torrence and G. Compo,
%      and is available at URL: http://paos.colorado.edu/research/wavelets/''.
%
% Reference: Torrence, C. and G. P. Compo, 1998: A Practical Guide to
%            Wavelet Analysis. <I>Bull. Amer. Meteor. Soc.</I>, 79, 61-78.
%
% Please send a copy of such publications to either C. Torrence or G. Compo:
%  Dr. Christopher Torrence               Dr. Gilbert P. Compo
%  Research Systems, Inc.                 Climate Diagnostics Center
%  4990 Pearl East Circle                 325 Broadway R/CDC1
%  Boulder, CO 80301, USA                 Boulder, CO 80305-3328, USA
%  E-mail: chris[AT]rsinc[DOT]com         E-mail: compo[AT]colorado[DOT]edu
%----------------------------------------------------------------------------
function [wave,period,scale,coi, dj,paramout,k] = ...
	contwt(Y,dt,pad,dj,s0,J1,mother,param)
if (nargin < 8), param = -1; end
if (nargin < 7) || isempty(mother), mother = -1; end
if (nargin < 6) || isempty(J1), J1 = -1; end %updated handling of defaults, JE oct 14 2014
if (nargin < 5) || isempty(s0), s0 = -1; end
if (nargin < 4) || isempty(dj), dj = -1; end
if (nargin < 3) || isempty(pad), pad = 0; end
if (nargin < 2)
	error('Must input a vector Y and sampling time DT')
end
n1 = length(Y);
if (s0 == -1), s0 = 2*dt; end
if (dj == -1), dj = 1./4.; end
if (J1 == -1), J1 = ceil((log(n1*dt/s0)/log(2))/dj); end  %changed fix to ceil(), JE Oct 12 2014
if (mother == -1), mother = 'MORLET'; end
%....construct time series to analyze, pad if necessary
x(1:n1) = Y - mean(Y);
if (pad == 1)
	base2 = fix(log(n1)/log(2) + 0.4999);   % power of 2 nearest to N
	x = [x,zeros(1,2^(base2+1)-n1)];
end
n = length(x);
%....construct wavenumber array used in transform [Eqn(5)]
k = [1:fix(n/2)];
k = k.*((2.*pi)/(n*dt));
k = [0., k, -k(fix((n-1)/2):-1:1)];
%....compute FFT of the (padded) time series
f = fft(x);    % [Eqn(3)]
%....construct SCALE array & empty PERIOD & WAVE arrays
scale = s0*2.^((0:J1)*dj);
period = scale;
wave = zeros(J1+1,n);  % define the wavelet array
wave = wave + 1i*wave;  % make it complex
% loop through all scales and compute transform
for a1 = 1:J1+1
	[daughter,fourier_factor,coi,dofmin, paramout]=wave_bases(mother,k,scale(a1),param);	
	wave(a1,:) = ifft(f.*daughter);  % wavelet transform[Eqn(4)]
end
period = fourier_factor*scale;
coi = coi*dt*[1E-5,1:((n1+1)/2-1),fliplr((1:(n1/2-1))),1E-5];  % COI [Sec.3g]
wave = wave(:,1:n1);  % get rid of padding before returning
return
% end of code